AMBER Archive (2006)

Subject: Re: AMBER: TI-FEP for ILE--->VAL.

From: David A. Case (
Date: Thu Aug 03 2006 - 11:43:44 CDT

On Thu, Aug 03, 2006, Biswa Ranjan Meher wrote:

> For our protein-drug system: we are doing the free energy perturbations in
> a transformation of ILE --->VAL using the TI method. We are using dummy
> atoms for the missing group -CH2 while transforming from ILE --> VAL.
> Regarding the force constants for bond, angle and dihedral parameters
> involving the dummy atoms - should it be same as in ILE?

Typically, one keeps the internal parameters for the dummy atoms the same as
in the real system; these terms should cancel on two sides of a thermodynamic
cycle. But this is not a requirement, and other dummy atom schemes are


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